Hi justin, My apologies for asking you so many small queries. Can you suggest any good tutorial or reference that talks about this issue of running MD over a selected part of molecule.
With Thanks, Vivek 2008/10/10 vivek sharma <[EMAIL PROTECTED]> > hI justin, > > Thanks for your response. > do I need to specify the index file(for residue that I want to keep fix > during MD) during GROMPP or just including the psre.itp in topology is > enough for the purpose ? > > > With Thanks, > Vivek > > 2008/10/10 Justin A. Lemkul <[EMAIL PROTECTED]> > >> >> >> Justin A. Lemkul wrote: >> >>> >>> >>> vivek sharma wrote: >>> >>>> Thanks Justin, >>>> >>>> My goal is to keep certain part fixed and move only a few of the >>>> residues (case is like providing flexibility to the site of interest only). >>>> SO , do I need to specify the residue using some index file ? >>>> or is there some other way to specify the part of molecule for position >>>> restraining ?? >>>> >>>> >> Make an index file with the residues you want to keep fixed, and pass it >> to genpr to generate a new posre.itp that corresponds to those residues. >> >> -Justin >> >> >>>> With Thanks, >>>> Vivek >>>> >>>> >>>> 2008/10/10 Justin A. Lemkul <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> >>>> >>>> >>>> >>>> vivek sharma wrote: >>>> >>>> Hi there, >>>> I want to run MD over a part of my molecule , for few residues >>>> only (not the whole molecule). >>>> Can I do it using GROMACS ? >>>> I searched for the online documentation and mailing list, but >>>> unable to get appropriate information. >>>> If somebody has already tried such things earlier, please >>>> suggest and direct me for appropriate link and address. >>>> >>>> >>>> Well, if your goal is to keep certain parts fixed and allow others >>>> to move, probably the easiest way to do it is to apply position >>>> restraints to the "fixed" part. >>>> >>>> -Justin >>>> >>>> With Thanks, >>>> Vivek >>>> >>>> >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> gmx-users mailing list gmx-users@gromacs.org >>>> <mailto:gmx-users@gromacs.org> >>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/search >>>> before posting! >>>> Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to [EMAIL PROTECTED] >>>> <mailto:[EMAIL PROTECTED]>. >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>> >>>> >>>> -- ======================================== >>>> >>>> Justin A. Lemkul >>>> Graduate Research Assistant >>>> Department of Biochemistry >>>> Virginia Tech >>>> Blacksburg, VA >>>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>>> >>>> ======================================== >>>> _______________________________________________ >>>> gmx-users mailing list gmx-users@gromacs.org >>>> <mailto:gmx-users@gromacs.org> >>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/search before >>>> posting! >>>> Please don't post (un)subscribe requests to the list. Use the www >>>> interface or send it to [EMAIL PROTECTED] >>>> <mailto:[EMAIL PROTECTED]>. >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>> >>>> >>>> >>> >> -- >> ======================================== >> >> Justin A. Lemkul >> Graduate Research Assistant >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [EMAIL PROTECTED] >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >
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